Modification of DNA structure by histone-like proteins appears to be a central regulatory mechanism governing the complex life cycle of Chlamydia trachomatis. These histone homologs, termed Hc1 and Hc2, are expressed only during the late stages of the chlamydial life cycle concomitant with the reorganization of RBs into EBs and play a major role in establishment of nucleoid structure as well as in control of gene expression. Expression of Hc1 in E. coli results in a compaction of the chromatin that ultrastructurally resembles the nucleoid reorganization which occurs late in the chlamydial developmental cycle and produces a global termination of transcription, translation, and replication at concentrations equivalent to that of chlamydial elementary bodies. The association of Hc1 with DNA at levels below that necessary to condense the nucleoid modifies DNA structure/topology to influence promoter activity and gene expression. Detailed biophysical analysis of Hc1-DNA interaction, in vitro, indicate that Hc1 preferentially binds supercoiled DNA. These results imply that Hc1 selectively stabilizes DNA of specific superhelical densities to modify DNA topology. The binding of Hc1 to DNA has been characterized to examine the effects of pH, reducing conditions, and ionic strength on the interaction. Ionic strength had a marked influence on both DNA-binding and DNA-dependent aggregation of the protein. Reversibility of this aggregation was also ionic strength dependent with a discrete optimum ionic strength for maintaining stable association. Hc1 associates with either positively or negatively supercoiled DNA in preference to relaxed DNA implying that the protein has the ability to discriminate between DNA domains of differing topology in vivo. Hc1-mediated effects on DNA topology may thus play a significant role in the regulation of gene expression during chlamydial development. Understanding the controlling mechanisms for gene expression and differentiation may suggest unique methods of interrupting parasite replication.